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src/c/o/cogent-1.5.3/tests/test_app/test_clustalw.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.clustalw import Clustalw, alignUnalignedSeqsFromFile,\
    alignUnalignedSeqs, alignTwoAlignments, addSeqsToAlignment,\
    buildTreeFromAlignment, build_tree_from_alignment, \
    def test_alignUnalignedSeqs(self):
        """Clustalw alignUnalignedSeqs should work as expected"""
        res = alignUnalignedSeqs(self.seqs1,WorkingDir='/tmp/ct')
        self.assertNotEqual(res['StdErr'],None)
        self.assertEqual(cw_vers.sub("", res['Align'].read()),
 
        #suppress stderr and stdout
        res = alignUnalignedSeqs(self.seqs1,WorkingDir='/tmp/ct',\
            SuppressStderr=True,SuppressStdout=True)
        self.assertEqual(res['StdOut'],None)

src/p/y/pycogent-HEAD/tests/test_app/test_clustalw.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.clustalw import Clustalw, alignUnalignedSeqsFromFile,\
    alignUnalignedSeqs, alignTwoAlignments, addSeqsToAlignment,\
    buildTreeFromAlignment, build_tree_from_alignment, \
    def test_alignUnalignedSeqs(self):
        """Clustalw alignUnalignedSeqs should work as expected"""
        res = alignUnalignedSeqs(self.seqs1,WorkingDir='/tmp/ct')
        self.assertNotEqual(res['StdErr'],None)
        self.assertEqual(cw_vers.sub("", res['Align'].read()),
 
        #suppress stderr and stdout
        res = alignUnalignedSeqs(self.seqs1,WorkingDir='/tmp/ct',\
            SuppressStderr=True,SuppressStdout=True)
        self.assertEqual(res['StdOut'],None)